Variant 16-11927438-ATGG-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP3BP6_ModerateBS1BS2

The NM_001396485.1(NPIPB2):c.1126_1128delCCA(p.Pro376del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00919 in 142,928 control chromosomes in the GnomAD database, including 13 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0092 ( 13 hom., cov: 31)

Exomes 𝑓: 0.0033 ( 29 hom. )

Failed GnomAD Quality Control

Consequence

NPIPB2
NM_001396485.1 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0890

Variant links:

Genes affected

NPIPB2 (HGNC:37451): (nuclear pore complex interacting protein family member B2) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

NPIPB2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001396485.1

BP6

Variant 16-11927438-ATGG-A is Benign according to our data. Variant chr16-11927438-ATGG-A is described in ClinVar as [Likely_benign]. Clinvar id is 2646232.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00919 (1313/142928) while in subpopulation SAS AF= 0.0235 (110/4690). AF 95% confidence interval is 0.0199. There are 13 homozygotes in gnomad4. There are 665 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 13 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NPIPB2	NM_001396485.1 link	c.1126_1128delCCA	p.Pro376del	conservative_inframe_deletion	8/8	ENST00000399147.8	NP_001383414.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
NPIPB2	ENST00000399147.8 link	c.1126_1128delCCA	p.Pro376del	conservative_inframe_deletion	8/8	5	NM_001396485.1	ENSP00000382101.4	A6NJ64
NPIPB2	ENST00000547494.6 link	c.1075_1077delCCA	p.Pro359del	conservative_inframe_deletion	8/8	5		ENSP00000448752.2	F8VY45
NPIPB2	ENST00000698171.1 link	c.1024_1026delCCA	p.Pro342del	conservative_inframe_deletion	7/7			ENSP00000513593.1	A0A8V8TLJ1
NPIPB2	ENST00000673243.1 link	c.706_708delCCA	p.Pro236del	conservative_inframe_deletion	10/10			ENSP00000500799.1	A0A5F9ZI19

Frequencies

GnomAD3 genomes

AF:

0.00914

AC:

1305

AN:

142840

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00391

Gnomad AMI

AF:

0.00221

Gnomad AMR

AF:

0.0108

Gnomad ASJ

AF:

0.0122

Gnomad EAS

AF:

0.000392

Gnomad SAS

AF:

0.0232

Gnomad FIN

AF:

0.00528

Gnomad MID

AF:

0.00980

Gnomad NFE

AF:

0.0117

Gnomad OTH

AF:

0.00656

GnomAD3 exomes

AF:

0.00298

AC:

442

AN:

148460

Hom.:

AF XY:

0.00274

AC XY:

218

AN XY:

79692

show subpopulations

Gnomad AFR exome

AF:

0.00119

Gnomad AMR exome

AF:

0.00192

Gnomad ASJ exome

AF:

0.00192

Gnomad EAS exome

AF:

0.0000898

Gnomad SAS exome

AF:

0.00511

Gnomad FIN exome

AF:

0.00136

Gnomad NFE exome

AF:

0.00368

Gnomad OTH exome

AF:

0.00406

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00334

AC:

3573

AN:

1071148

Hom.:

AF XY:

0.00367

AC XY:

1986

AN XY:

541762

show subpopulations

Gnomad4 AFR exome

AF:

0.00120

Gnomad4 AMR exome

AF:

0.00233

Gnomad4 ASJ exome

AF:

0.00572

Gnomad4 EAS exome

AF:

0.000116

Gnomad4 SAS exome

AF:

0.00821

Gnomad4 FIN exome

AF:

0.00704

Gnomad4 NFE exome

AF:

0.00284

Gnomad4 OTH exome

AF:

0.00387

GnomAD4 genome

AF:

0.00919

AC:

1313

AN:

142928

Hom.:

Cov.:

AF XY:

0.00951

AC XY:

665

AN XY:

69910

show subpopulations

Gnomad4 AFR

AF:

0.00407

Gnomad4 AMR

AF:

0.0108

Gnomad4 ASJ

AF:

0.0122

Gnomad4 EAS

AF:

0.000393

Gnomad4 SAS

AF:

0.0235

Gnomad4 FIN

AF:

0.00528

Gnomad4 NFE

AF:

0.0117

Gnomad4 OTH

AF:

0.00699

Alfa

AF:

0.0141

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2023

NPIPB2: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over